Contents

Transcription Initiation in Prokaryotes

A bacterial gene may have the following regulatory sequences that are involved in transcription: a promoter sequence, found upstream (before) the start of the gene coding sequence, and a terminator sequence, found downstream (past the end) of the end of the gene coding sequence.

RNA polymerase is used to synthesize RNA by interacting with the DNA and "reading" it as a template. During initiation of transcription, RNA polymerase needs to bind to a promoter. There are many different promoters. In prokaryotes, the σ-factor assists RNA polymerase in recognizing a specific promoter. As there are many different promoters, there are many different σ-factors that recognize specific sequences in specific promoters.

Some common bacterial promoter sequences include 5'-TTGACA-3' at the -35bp region (-35 means 35 bp from the start of the coding sequence, and there is no "0bp", it goes from "-1bp" to "1bp") and 5'-TATAAT-3', formerly called the Pribnow box, located at the -10bp region. When transcription initiation occurs, RNA polymerase in complex with the σ-factor binds tightly to the -10bp region and more loosely with the -35bp region. This complex is called the closed promoter complex because the DNA has not been unwound yet.

RNA synthesis--Prokaryotes

In order for RNA synthesis to occur, the DNA has to be denatured. Once the DNA is denatured about 10 base pairs before the start site, the RNA polymerase complex is called an open promoter complex. Note that the σ-factor is not actually required for RNA synthesis, and it is released after a few base pairs of RNA are synthesized. RNA is synthesized from 5'-3', and the DNA template is read from 3'-5'. As elongation occurs, the RNA polymerase untwists the downstream dsDNA, and the upstream dsDNA renatures..

Transcription Termination--Prokaryotes

Terminator sequences signal the stoppage of transcription. There are two types of transcription termination: ρ-independent and ρ-dependent. A ρ-independent terminator is a GC-rich sequence, and its transcription causes the mRNA to loop over. The looping slows and eventually stops RNA polymerase from transcribing, and RNA polymerase eventually dissociates from the DNA template. A ρ-dependent terminator does not use hairpin looping to prevent RNA polymerase activity; rather, the ATP-dependent protein Rho binds to the RNA transcript and travels up the RNA transcript, binds to RNA polymerase, and stops transcription. Rho does this by acting as a helicase, unwinding the RNA-DNA complex, thus causing RNA strand to be released, allowing renaturation of the DNA strands and dissociation of the RNA polymerase from the DNA strand.